windows-specific-functions: Windows specific functions.

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

Windows specific functions.

Description

The functions runXmlMethodChanger and runScanHeadsman call XmlMethodChanger.exe and ScanHeadsman.exe with the corresponding arguments. The only work on Windows (maybe on Linux + wine as well but that was never tested).

Usage

createTngFusionMethFiles(
  template,
  xml = list.files(pattern = ".*\\.xml$"),
  executable = "XmlMethodChanger.exe",
  verbose = interactive()
)

runXmlMethodChanger(
  template,
  xml = list.files(pattern = ".*\\.xml$"),
  executable = "XmlMethodChanger.exe",
  verbose = interactive()
)

runScanHeadsman(path = ".", executable = "ScanHeadsman.exe")

Arguments

template	character, path to template .meth file.
xml	character, vector of path to .xml files.
executable	character, path to the XmlMethodChanger.exe or ScanHeadsman.exe executable.
verbose	logical, if TRUE a progress bar is shown.
path	character, path to the directory containing the .raw files.

Details

runXmlMethodChanger applies ‘XmlMethodChanger.exe’ on all given XML files generated with writeMethodXmls() to create .meth files from a template.

runScanHeadsman calls ScanHeadsman.exe on a given directory containing .raw files. ScanHeadsman.exe extracts the method and scan header data into .experiments.csv and .txt files, respectively.

Value

Nothing. Used for its side effects.

References

XmlMethodChanger source code: https://github.com/thermofisherlsms/meth-modifications/

ScanHeadsman source code: https://bitbucket.org/caetera/scanheadsman

See Also

writeMethodXmls()

Examples

## Not run: 
runXmlMethodChanger(templateMeth="TMS2IndependentTemplate240Extended.meth",
                    modificationXml=list.files(pattern="^method.*\\.xml$"),
                    executable="..\\XmlMethodChanger.exe")

## End(Not run)
## Not run: 
runScanHeadsman("raw", executable="..\\ScanHeadsman.exe")

## End(Not run)

sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.